Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• MACSIMS: multiple alignment of complete sequences information management system.

  PMID 16792820 · PMC1539025 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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  MACSIMS is a multiple alignment-based information management system combining knowledge-based database mining with ab initio sequence predictions

  balibase-derived sequences same query automatic database initio

• Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.

  PMID 34489462 · PMC8421402 · Scientific data · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  Chromosome-scale genomes of six Leishmaniinae species (five L. (Mundinia) species and one Porcisia species) were sequenced, assembled and annotated, providing genome, proteome, transcriptome and GFF outputs for taxa previously lacking public reference genomes

  six same polished each nanopore illumina novo

• Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

  PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  829 genes are overexpressed in the oscular region of increased calcite spicule formation in S. ciliatum

  sycon ciliatum sponges differential go-term genome

• Functional classification using phylogenomic inference.

  PMID 16846248 · PMC1484587 · PLoS computational biology · 2006 · 8 claims · 1 setups

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  Functional annotation via top-hit database search transfer is used far more often in practice than phylogenomic inference, despite phylogenomic inference being more accurate.

  uniprot database

• LMPD: LIPID MAPS proteome database.

  PMID 16381922 · PMC1347484 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  LMPD is an object-relational database of lipid-associated protein sequences and annotations, publicly available from the LIPID MAPS Consortium website.

  uniprot kegg in-house oracle9i kegg database enzyme

• The Edinburgh human metabolic network reconstruction and its functional analysis.

  PMID 17882155 · PMC2013923 · Molecular systems biology · 2007 · 8 claims · 7 setups

  Full-text index only

  EHMN is a high-quality, manually curated human metabolic network combining genome-based and literature-based (EMP) reconstruction, containing nearly 3000 reactions and over 2000 metabolic genes.

  enzyme emp kegg humancyc genome literature-based comparative

• DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.

  PMID 17980028 · PMC2186358 · BMC bioinformatics · 2007 · 7 claims · 3 setups

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  The DAVID Gene Concept, a single-linkage algorithm, merges gene clusters from Entrez Gene, UniRef100, and PIR-NREF100 that share protein IDs and species into unified DAVID gene clusters, improving cross-referencing between NCBI and UniProt systems

  members entire usp8 sequence annotation

• MODBASE: a database of annotated comparative protein structure models and associated resources.

  PMID 16381869 · PMC1347422 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  MODBASE is a database of automatically calculated comparative protein structure models covering all UniProt sequences matchable to a known structure

  uniprot non-redundant complexes saccharomyces comparative pairwise domain-domain

• Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.

  PMID 16034025 · PMC1179732 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  Partial EC numbers are semantically ambiguous, and databases that assign a gene to all reactions sharing the same partial EC number make a faulty inference, causing systematic misannotation.

  e.coli biocyc vimss specific database comparative manual

• DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.

  PMID 17576678 · PMC1933169 · Nucleic acids research · 2007 · 8 claims · 4 setups

  Full-text index only

  The DAVID Gene Concept uses a single-linkage method to agglomerate tens of millions of gene/protein identifiers from NCBI, PIR, UniProt and other resources into unified DAVID genes.

  gene example gene single-linkage functional

• MODBASE, a database of annotated comparative protein structure models and associated resources.

  PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

  sequences chains template chain comparative pairwise ligand

• Recent additions and improvements to the Onto-Tools.

  PMID 15980579 · PMC1160233 · Nucleic acids research · 2005 · 7 claims · 3 setups

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  The Onto-Tools back-end database was redesigned around the Entrez Gene data model after NCBI phased out LocusLink in February 2005.

  homo example mus functional pathway cross-database

• The Vertebrate Genome Annotation (Vega) database.

  PMID 15608237 · PMC540089 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Vega is a community database for browsing manual annotation of finished vertebrate genome sequences, based on an extended Ensembl-style schema.

  chromosomes genomic manual sequence initio

• Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

  PMID 16246909 · PMC1266070 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  The BioCyc collection has been expanded to 160 pathway/genome databases (PGDBs) organized into three curation tiers.

  sequenced cmr-derived uniprot cogent computational genome sequence

• 'Genome design' model and multicellular complexity: golden middle.

  PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

  normal genes proteins encoded oligonucleotide gene functional

• An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

  PMID 19091018 · PMC2638159 · BMC bioinformatics · 2008 · 6 claims · 5 setups

  Full-text index only

  Existing SNP/disease databases are fragmented; no combined resource widely supports gene-, SNP-, and disease-related information together

  private disease uniprot snps database controlled sequence

• Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

  PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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  Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

  species genomic jmjd6 jmjc reciprocal comparative est

• BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.

  PMID 17202167 · PMC1899097 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  BRENDA is the largest publicly available enzyme information system worldwide, manually curated from primary literature and covering all identified enzymes regardless of source.

  pubmed randomly enzyme full text-mining manual transmembrane